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Lecture 6

BI110 Lecture 6: Biology Note 6 (Modules 3-12)

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Matthew Smith

Module 3: Practicing Biology Describe the scientific method - Science: is a way of learning about the universe through a formal process of observation and experimentations called scientific method - Inductive Reasoning: general conclusions are drawn from specific observations - Deductive reasoning: specific results are predicted from a general premise. * Inductive reasoning (bright colour must come from competitive advantage) leads to deductive reasoning (the parents feed brightly coloured chicks) - Hypothesis: an answer to a well-framed question(formed so that it can be proved wrong) Describe how data are analyzed 2 types of data 1. Experimental group: receives treatment 2. Control group: does not receive treatment * an experiment where one group receives treatment and the other does not is called a controlled experiment  independent variable: the variable that differs between the experimental group and the control group; the one that is controlled by the scientist  defendant variable: data collected in an experiment (they depend on the independent variable) Describe different types of experimental setups - Unit intentional bias of the scientist or human tester can potentially skew results for this reason, most studies are double blind: neither the researcher nor the test subjects know who is in the experimental group and who is in the control group. Different types of experimental setups include: *everybody should be similar in age, sex, health, ect. 1. Natural experiments  2 existing natural populations are compared (smokers/non-smokers) 2. Regression analysis  varying levels of treatment are applied to test subjects (drugs) 3. Active controlled experiments  the experimental group is given a new treatment Module 4: Atoms, Elements, and Matter Distinguish between atoms and elements - Living organism are composed of elements, molecule and matter - Atom: smallest particle of an element that has the properties of that element - Element: a pure substance made up of one kind of atom that cannot be broken down into simpler substances. (example Au = gold) Identify the main essential elements in all living organisms and discuss the role of trace elements: - The compounds found in living organisms are composed of only a small subset of the elements found on Earth: 1. Hydrogen (H) 2. Carbon (C) 3. Nitrogen (N) 4. Oxygen (O) - These elements make up more than 95% of all matter found in living organisms. 5. Calcium (Ca) 6. Sulfur (s) 7. Phosphorus (P) - These elements bring the percentage to more than 99 percent - These 7 are the most abundant in living organisms - There are about 25 elements that are necessary for humans to function properly (ones not named are called trace elements – not needed in big amounts) Summarize the simplified atomic model and describe its limitations: - John Dalton created atomic model - The properties of elements depend on atomic structure  Protons: +ve charged particles in the atomic nucleus =dense center of the atom (located in the nucleus) Neutrons: electrically neutral (located in the nucleus) (# of protons – mass #)  Electrons: surround the nucleus and have –ve charged (protons = electrons) - Most of an atoms mass is in the nucleus - Atomic number: # of protons - Mass number: # of protons plus the number of neutrons (# of electrons – # of protons) - Isotopes: atoms that have the same # of protons but diff # of neutrons (like Cl) - Noble Gases: an element with a full outer electron shell Explain how the number of electrons in valence shells determines the chemical behavior of an atom: - Electrons exist in energy levels called Electron Shells (n-1, n-2, n-3) - Each shell can only hold a certain number of electrons - The energy of electrons increases with the size of the shell. - N-1 allows 2 electrons N-2 allows 8 electrons N-3 allows 18 electrons - When the shell has a complete number of electrons, the element is stable and is not likely to react with other atoms/elements - Valence electrons are located in the outermost shell  an atoms reactivity depends on if that outer shell is full or not Module #5: Structures of molecules and compounds Distinguish between molecules and compounds: - Molecule: when 2 or more atoms of the same element combine (example 02 = oxygen) - Compounds: when molecules consist of more than one element (example CO2 = carbon dioxide) - Chemical bonds: how compounds are held together; they form because a full valence shell is more stable than a partly filled one - There are different types of chemical bonds (bonds vary in strength – that is the amount of energy required to break the bond): 1. Covalent bonds – strong ; form when 2 non-metals share electrons -single bond  forms between 2 atoms that share one pair of electrons -double bond  forms between 2 atoms that share 2 pairs of electrons - non polar covalent bonds  2 non-metals with similar electronegs share electrons equally (O2) -polar covalent bond  form between 2 atoms with opposite elecrtonegs (H2O) 2. Ionic bonds –strong; forms between a non-metal and a metal; electrons transfer from metal (get +ve charge and becomes a cation)to non-metals (get –ve charge and becomes an anion) 3. Hydrogen bonds – weak; occur when molecules have hydrogen covalently bonded to oxygen, nitrogen, or fluorine interact 4. Van der Waals forces - weak; redistribution of charge that causes neighboring atoms to attract one another - Electronegativity: ability of an atom to attract electrons; the greater the electroneg, the more attraction an atom has for electrons Explain what intermolecular forces are: - Non covalent (weak) attractions between molecules are called intermolecular forces. 2 diff types: 1. Hydrogen bonds 2. Van der Waals Relate the importance of chemical bonds and chemical reactions to life processes: - Chemical reaction: occurs when chemical bonds are made or broken. - Reactants: the ingredients in the chemical reaction - Product: the reactants combine to form this - Example of a chemical reaction in all living organisms = the making of ATP ATP breakdown = exergonic  ATP synthesis = endergonic Describe the properties of carbon that allow it to form organic molecules: - Carbon atoms have 4 electrons in its outer shell therefore allowing it to form connections with 4 other atoms. (a lot of molecules can be formed like, organic compounds –which contain a hydrogen and a carbon) an organic compound arises when carbon, hydrogen and sometimes another element form covalent bonds an organic compound composed of only hydrogen and carbon is a hydrocarbon - Isomers: compounds with the same number of atoms and the same element but just structured differently (cis & trans) - Carbon can form double & single bonds Summarize the Miller-Urey experiment and its significance: - Produced complex organic compounds from inorganic compounds - Goal: understand how life first formed - Data: under certain Earth conditions, inorganic compounds could react to form amino acids and hydrocarbons Module 6: Water Describe the basic properties of water molecules: - Our bodies contain more water than any other compound; water is the most abundant compound on Earth - Water is the only natural substance that exists in 3 states: gas, liquid, solid within earths normal temp. - Water has a high specific heat: how much heat must be gained or lost to change the temperature of a substance (therefore water stores a lot of thermal energy) - Water is less dense as a solid than as a liquid (because of air bubbled in ice – allowing it to float) - Water is a UNIVERSAL SOLVENT Water molecules are small, bent and polar: - Water molcelules consist of 2 hydrogen atoms and 1 oxygen atom - Oxygen atom is much more electornegative (aka attract more electrons)(-ve) than a hydrogen (+ve) atom ;therefore the bond between oxygen and hydrogen is polar covalent . - Water molecule is a dipole: a structure with +ve and –ve poles (polar molecule) Explain how the polarity of water molecules results in hydrogen bonding: - The slight +ve charge on the hydrogen atoms of one water molecule attracts the slght –ve charge on the oxygen atoms of other water molecules forming intermolecular forces called hydrogen bonding - Water is a liquid at room temperature because of hyrodgen bond interactions between molecules Summarize the unique properties of water that are important for sustaining life: - 4 most important properties of water: 1. Water is “sticky” surface tension: the ability of the surface of a liquid to resist penetration -the surface tension in water is high because hydrogen bonds are formed easier in water than in air 2. Water is an excellent solvent Solution (sea water): a mixture of 2 or more substances; solvent & solutes (the solutes dissolve in the solvent.  the polarity of water molecules enables them to attract other polar substances which makes those substances dissolve  hydrophobic (doesn’t dissolve in water -fats ) hydrophilic (dissolve in water) – cell membrane, therefore important to life, because all life is made of cells. 3. Water moderates temperature Heat: total kinetic energy (movement)  Temperature: average kinetic energy  a given mass of water must gain a lot of heat to increase in temperature evaporative cooling: a reduction of temperature caused by evaporation (sweating) 4. Ice (solid water) floats on liquid water  as water freezes, the solid form of water expands; and becomes less dense; therefore fewer water molecules in the same volumes Module #7: Aqueous Solutions, Acids, and Bases Understand pH and how acids and bases interact with water - Acid: a substance that increases the concentration of H20 in a solution (has more H2O than OH); acids can be strong or weak; Sour taste = acids - Base: a substance that decreases the concentration of H20 in a solution (has more OH than H20); bases can be strong or weak; Bitter taste = bases - Pure solution has equal amounts of H2O and OH - pH scale ranges from 0-14 (it is a log scale)  water has a pH of 7  the lower the pH the more acidic the solution/ the higher the pH, the more alkaline the solution  basic solutions have a pH greater than 7 Describe how a buffer contributes to pH stability - Buffer: a substance that minimizes change in pH. - Weak acids and weak bases act as buffers in aqueous solution - A reaction between CO2 and H2O forms carbonic acid (weak acid)  if H is added to a carbonic acid solution, it reacts with CO3 and HCO3 which drives the reaction to the left. If OH is added it removes H from the solution which pulls the reaction to the right.  therefore the carbonic acid is acting as a buffer in this case (bc it can remove H and OH from the solutions) Understand how pH affects organisms and ecosystems - pH gradients across intracellular compartments are necessary for many cellular functions; prokaryotic and eukaryotic pH’s are carefully regulated - Pollutants undergo chemical reactions that produce carbonic/sulfuric/nitiric acids  these acids react with water to form acid precipitation  pH = 4.2-5.0 -acid rain leaches nutrients from the soil/ can kill tress/ affects aquatic systems - Rain water is normally already acidic due to the presence of CO2  pH = 5.6 - Acid remediation :deposit CO3 into streams which raises their pH (good thing) Understand the mole, and describe various units of concentration - Often scientists want to know how many particles of solute are present. Particles may be atoms, molecules, or units of ionic compound - The number of particles can be calculated using a value called the mole  one mole contains 6.02 X 10^23 - Mass of one mole of an element equals its atomic mass in grams (Example: NA atomic mass = 23, so one mole of NA = 23g) - Molar Mass of a compound equals the combined mass of its component atoms. (Example:NaCl  Cl atomic mass= 35, Na atomic mass = 23 23+35=58g/mol) - Molar concentration: the number of solute in a given volume of water (units = moles/litre =molarity) Module #8: Carbohydrates Classify monosaccharides based on molecular characteristic - Monosacchrides are the simplest type of carbohydrate (simple sugars) - Glucose is the basic energy source for the cell (in humans) - Functions of monosaccharides: provides chemical energy to cells and serves as a building block in the synthesis of larger molecueles. - Monosaccharides are made up of 3-7 carbon atoms connected in a chain (can form rings if want to be more stable in an aqueous solution). - A carbonyl group is attached to one of the carbons and a hydroxyl group is attached to each of the others - 3 ways we classify monosaccharides: 1. The precise location of the carbonyl group carbonly group on a terminal carbon = aldehyes  carbonyl group is boneded to 2 other carbons in the middle = ketone 2. The length of carbon skeleton  can range from 3-7 carbons 3. The arrangement of the hydroxyl groups around the carbons  Example: glucose and galactose are both very similar in formula and structures. The difference between them is the orientation of the middle hydroxyl group Relate structures of oligosaccharides and polysaccharides to their function in cells and organisms - Monosaccharides are joined together resulting in polymers  polysaccharides and oligosaccharides (can serve as energy storage, structural elements of cells, or signaling and cell recognition) - Polysaccharides serve 2 functions in organism: 1. Energy storage (animals store glucose as glycogen (a-glucose)/plants store it as starch (a-glucose)) 2. Structural support (cellulose chain of hundreds of glucose monomers (b-glucose_) 3. Oligosaccharides: signal and recognition of cells use glycoproteins to recognize Explain how a glyscosidic linkage forms by a dehydration synthesis reaction - Glyscosidic linkage = a covalent bond that can connect 2 monosaccharides together; OH is lost
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